PyRank

Multiplexed Imaging Python Packages

Python packages with the GitHub topic multiplexed-imaging. Sorted by monthly downloads, with stars and forks.
prism-oncology
sopa

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)

3K 296 52
angelolab
ark-analysis

Integrated pipeline for multiplexed image analysis

2K 108 31
camlab-bioml
astir

astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨

683 57 13
calico
spatial-lda

Probabilistic topic model for identifying cellular micro-environments.

594 28 12
nadeemlab
spatialprofilingtoolbox

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io) [NeurIPS'26]

589 23 2
complextissue
spatiomic

A Python package for unsupervised analysis of spatial (prote)omics data.

353 19 0
AlanRace
pyimc

Rust library for reading imaging mass cytometry (IMC) data stored in .mcd files.

237 2 0
JoshuaHess12
hdi-utils

General importing and utility functions for high-dimensional image data

105 0 0
nadeemlab
smprofiler

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io) [NeurIPS'26]

70 23 2
JoshuaHess12
miaaim-python

MIAAIM: Multi-omics Image Alignment and Analysis by Information Manifolds

30 5 1